[English] 日本語
Yorodumi
- PDB-4x6d: CD1a ternary complex with endogenous lipids and BK6 TCR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4x6d
TitleCD1a ternary complex with endogenous lipids and BK6 TCR
Components
  • Beta-2-microglobulin
  • T-cell surface glycoprotein CD1a
  • TCR alpha
  • TCR beta
KeywordsIMMUNE SYSTEM / CD1a / TCR / Immune complex / Lipid antigen
Function / homology
Function and homology information


exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules ...exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / Co-inhibition by PD-1 / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / response to bacterium / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / Downstream TCR signaling / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endosome membrane / immune response / membrane raft / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
MHC-I family domain / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily ...MHC-I family domain / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
OLEIC ACID / PALMITOLEIC ACID / T cell receptor alpha chain constant / T cell receptor beta constant 1 / T-cell surface glycoprotein CD1a / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsBirkinshaw, R.W. / Rossjohn, J.
CitationJournal: Nat.Immunol. / Year: 2015
Title: alpha beta T cell antigen receptor recognition of CD1a presenting self lipid ligands.
Authors: Birkinshaw, R.W. / Pellicci, D.G. / Cheng, T.Y. / Keller, A.N. / Sandoval-Romero, M. / Gras, S. / de Jong, A. / Uldrich, A.P. / Moody, D.B. / Godfrey, D.I. / Rossjohn, J.
History
DepositionDec 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Mar 4, 2015Group: Structure summary
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / entity / entity_src_gen / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.entity_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_asym.entity_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: T-cell surface glycoprotein CD1a
B: Beta-2-microglobulin
C: T-cell surface glycoprotein CD1a
D: Beta-2-microglobulin
E: TCR alpha
F: TCR beta
G: TCR alpha
H: TCR beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,50212
Polymers187,8248
Non-polymers1,6784
Water181
1
A: T-cell surface glycoprotein CD1a
B: Beta-2-microglobulin
G: TCR alpha
H: TCR beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7656
Polymers93,9124
Non-polymers8532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: T-cell surface glycoprotein CD1a
D: Beta-2-microglobulin
E: TCR alpha
F: TCR beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7376
Polymers93,9124
Non-polymers8252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.133, 126.322, 226.852
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 4 types, 8 molecules ACBDEGFH

#1: Protein T-cell surface glycoprotein CD1a / T-cell surface antigen T6/Leu-6 / hTa1 thymocyte antigen


Mass: 31567.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P06126
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P61769
#3: Protein TCR alpha


Mass: 22998.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01848*PLUS
#4: Protein TCR beta


Mass: 27597.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01850*PLUS

-
Sugars , 1 types, 2 molecules

#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

-
Non-polymers , 3 types, 3 molecules

#6: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#7: Chemical ChemComp-PAM / PALMITOLEIC ACID


Mass: 254.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H30O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Nonpolymer detailsOleic acid (OLA) and palmitoleic acid (PAM) associated with CD1a in this entry represent the ...Oleic acid (OLA) and palmitoleic acid (PAM) associated with CD1a in this entry represent the minimal conserved acyl chains that fit the lipid electron density from array of potential phospholipids

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium citrate, bis-tris propane, PEG 3350 / PH range: 6-6.7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.98→48.48 Å / Num. obs: 53826 / % possible obs: 99.7 % / Redundancy: 17.5 % / Net I/σ(I): 16.4
Reflection shellResolution: 2.98→3.07 Å / Redundancy: 17.5 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 4439 / % possible all: 96.5

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Chain A and B from 1ONQ and chain G+H from 4PJ5

1onq

4pj5


Resolution: 2.98→48 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 2661 4.96 %
Rwork0.177 --
obs0.18 53686 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.98→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12189 0 114 1 12304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812661
X-RAY DIFFRACTIONf_angle_d1.10517171
X-RAY DIFFRACTIONf_dihedral_angle_d15.1554553
X-RAY DIFFRACTIONf_chiral_restr0.0451828
X-RAY DIFFRACTIONf_plane_restr0.0052206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.98-3.03420.35741230.29132613X-RAY DIFFRACTION99
3.0342-3.09260.31451510.26132661X-RAY DIFFRACTION100
3.0926-3.15570.35251230.24622666X-RAY DIFFRACTION100
3.1557-3.22430.29411310.23262656X-RAY DIFFRACTION100
3.2243-3.29930.30221230.22382646X-RAY DIFFRACTION100
3.2993-3.38170.29621240.2042674X-RAY DIFFRACTION100
3.3817-3.47320.25611410.19072671X-RAY DIFFRACTION100
3.4732-3.57530.2571400.18552640X-RAY DIFFRACTION100
3.5753-3.69070.23911330.17642670X-RAY DIFFRACTION100
3.6907-3.82250.23341380.17192689X-RAY DIFFRACTION100
3.8225-3.97550.19831600.16262643X-RAY DIFFRACTION100
3.9755-4.15640.2141580.15072639X-RAY DIFFRACTION100
4.1564-4.37540.20011530.14012675X-RAY DIFFRACTION100
4.3754-4.64930.16621630.12512659X-RAY DIFFRACTION100
4.6493-5.00790.19461310.12822743X-RAY DIFFRACTION100
5.0079-5.51120.19571340.15062701X-RAY DIFFRACTION100
5.5112-6.30720.25081400.18062732X-RAY DIFFRACTION100
6.3072-7.94050.25411430.2022747X-RAY DIFFRACTION100
7.9405-48.00760.21851520.20082900X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5245-0.274-0.49255.5388-4.83173.22610.14590.06670.0462-0.4946-0.5289-0.51880.29710.3630.31090.80410.06960.07330.86050.2180.651-20.5319-52.001454.205
23.3165-1.02440.22544.2799-0.53261.055-0.0939-0.0880.38930.6454-0.4284-1.57280.88621.02720.41541.43230.2871-0.1611.45760.60121.0492-7.8252-59.052765.6975
32.14791.2454-0.78164.728-2.70173.64210.1624-0.0196-0.38960.25810.43170.60440.2316-0.7522-0.59160.7482-0.0572-0.0280.64350.2361.0107-22.9794-75.9384-3.1428
42.42611.7909-1.10044.986-1.7324.2345-0.23430.3281-0.4051-0.38820.66511.26461.472-1.4164-0.37251.3044-0.3741-0.21191.03530.49721.5602-33.5051-93.30734.0812
52.2848-0.6889-0.05336.8453-3.26553.1765-0.04170.26430.2664-0.0285-0.0062-0.2617-0.44810.20320.04810.4454-0.1064-0.13560.57190.02150.4546-9.037-33.1068-28.6559
63.2520.5261-0.96153.0998-1.141.8080.08830.16960.2033-0.2508-0.17530.1779-0.2187-0.06290.08070.46580.0465-0.20060.5847-0.02110.524-28.9814-28.3512-27.8257
72.37360.0863-0.51055.3761-3.90775.0820.01340.20310.288-0.4242-0.07620.35680.0387-0.04730.03880.38250.0109-0.03610.4685-0.03550.5704-31.6365-11.177912.485
83.2645-1.82810.78033.9343-1.99282.81390.0280.14850.3724-0.2253-0.1642-0.0879-0.20660.22190.10330.3632-0.0964-0.01960.48290.06330.5015-12.5683-12.1688.8005
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN 'A' AND RESID 7 THROUGH 278)
2X-RAY DIFFRACTION2(CHAIN 'B' AND RESID 1 THROUGH 95)
3X-RAY DIFFRACTION3(CHAIN 'C' AND RESID 7 THROUGH 268)
4X-RAY DIFFRACTION4(CHAIN 'D' AND RESID 1 THROUGH 96)
5X-RAY DIFFRACTION5(CHAIN 'E' AND RESID 2 THROUGH 201)
6X-RAY DIFFRACTION6(CHAIN 'F' AND RESID 3 THROUGH 243)
7X-RAY DIFFRACTION7(CHAIN 'G' AND RESID 2 THROUGH 201)
8X-RAY DIFFRACTION8(CHAIN 'H' AND RESID 3 THROUGH 244)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more